Visible crew/equipment: When Ryback throws the exploding bomb into the car that the bad guys are in, one of the guys bursts into flames and you can see the white fire safety mask that he is wearing.
Visible crew/equipment: At the beginning of the film when all the personnel leave the control room, you can see the boom mike visible in the reflection at the top of the glass.
Visible crew/equipment: When the bad guys steal the helicopters and take off you can see the blades spinning at the top of the frame from the camera chopper during the wide shot of the other two choppers.
Answer: I would say yes they where planning on killing some of the mercs. There is one fact that shows that. if they had plan on putting all the mercs into the copter, then the guys in the engine car should have know at x time get out and move back to get into the copter, giving the fact that they are still in the engine car when it hits the other train tells me they didn't know.